Hi All How do I get from the probe set IDs in the AffyBatch@exprs to e.g. Genebank acc. numbers? I would like to be able to make the replacement using the .GIN file because I am also looking at custom affy chips. Thank you in advance. Best regards Jeppe

If you are using a custom chip (without an annotation package), you can probably do this using merge. See ?merge. Sean On Mar 3, 2005, at 5:57 AM, JSPC (Jeppe Skytte Spicker) wrote: > Hi All > > How do I get from the probe set IDs in the AffyBatch@exprs to e.g. > Genebank acc. numbers? > > I would like to be able to make the replacement using the .GIN file > because I am also looking at custom affy chips. > > Thank you in advance. > > Best regards Jeppe > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

On Thu, Mar 03, 2005 at 11:57:16AM +0100, JSPC (Jeppe Skytte Spicker) wrote: > How do I get from the probe set IDs in the AffyBatch@exprs to e.g. > Genebank acc. numbers? > > I would like to be able to make the replacement using the .GIN file > because I am also looking at custom affy chips. > > Thank you in advance. Hi Jeppe Everything is stored in so called annotation packages. The basic identifier is the probeset id, so everything maps from probeset id to various databases. If you are using hgu133a you load the metadata by > library(hgu133a) No yiu have a number of different envirnoment available, which corresponds to maps between probeset id and various databases. You can get an overview by > library(help = hgu133a) I am not an expert on these databases, but to me it dseems like you need the hgu133aACCNUM, you can read about it by > ? hgu133aACCNUM So how do you use it? Well, you take your favorite affy id, eg. by > id <- geneNames(data[i,]) (the i'the row) And then you do > get(id, envir = hgu133aACCNUM) This gives you the value. In case you need to look up several id's at the same time (which you usually do), you do > idmany <- geneNames(data[80:100,]) # caharcter vector > mget(idmany, envir = hgu133aACCNUM) These environmnets basically function like hash tables in perl, if you are familiar with those. If you need to build customn annotation, you need to use the AnnBuilder package. This is a big project, but certainly doable (I think :) Prepare to spend a lot of time reading the documentation. /Kasper -- Kasper Daniel Hansen, Research Assistant Department of Biostatistics, University of Copenhagen